Loading the library
library(Seurat)Setting the working directory
setwd("C:/Users/savill/OneDrive/Documents/PhD Jesse/R-Objects")Loading the data
# load my data
Gastruloid_72h_merged_afterQC <- readRDS("./df72v3.rds")
Gastruloid_72h_merged_afterQCAn object of class Seurat
36738 features across 1742 samples within 2 assays
Active assay: RNA (20186 features, 2000 variable features)
1 other assay present: SCT
2 dimensional reductions calculated: pca, umapDefaultAssay(Gastruloid_72h_merged_afterQC) <- "SCT"
Gastruloid_72h_merged_afterQC <- SetIdent(Gastruloid_72h_merged_afterQC, value = "predicted.id")Getting the metadata and taking a peak:
metadata <- Gastruloid_72h_merged_afterQC@meta.data
head(metadata)Get all the columns so we can delete the old morphology info:
colnames(metadata) [1] "orig.ident" "nCount_RNA" "nFeature_RNA" "Sample.barcode" "Morphotype" "percent.mt" "RNA_snn_res.0.3" "seurat_clusters"
[9] "S.Score" "G2M.Score" "Phase" "old.ident" "nCount_SCT" "nFeature_SCT" "predicted.id" "prediction.score.17"
[17] "prediction.score.8" "prediction.score.19" "prediction.score.3" "prediction.score.37" "prediction.score.13" "prediction.score.36" "prediction.score.33" "prediction.score.27"
[25] "prediction.score.12" "prediction.score.38" "prediction.score.7" "prediction.score.2" "prediction.score.11" "prediction.score.20" "prediction.score.16" "prediction.score.max"
[33] "Area" "AR" "percent.ribo" "RNA_snn_res.0.5" "RNA_snn_res.0.4" "celltype" "Emb_Stage" all_features = colnames(metadata)
old_morpho_features = c("Area","AR")
metadata_old_removed = metadata[!(all_features %in% old_morpho_features)]
#index_name = "row_names"
#metadata_old_removed[, index_name] <- rownames(metadata_old_removed)
metadata_old_removedNANow we can move on to loading the new features and adding them to the metadata:
my_data_72h = read.csv("Morphodata_All_Features_Sequenced_072h.csv")
dim(my_data_72h)[1] 48 537my_data_72hAdding the identifier so we can merge the dataframes:
# if this is how we add the barcode identifyer it is CRITICAL that the order is the same as in the spreadsheet
# This means A1-A12 INSTEAD of A10,A11,A12,A1,A2 (which is the default order in python and pandas)
barcoder_identifier = "bar"
my_data_72h[barcoder_identifier] <- paste("Bar", c(1:48), sep="")
my_data_72hHere I am basically excluding the columns we don’t want to add, assuming that we want to add all columns that are in the .csv file. Alternatively we could specify which columns (or which features) we want to add to the seurat object manually. No matter which way it is done we would have to add the sample barcode to be able to merge the data with the existing metadata.
all_columns = colnames(my_data_72h)
columns_we_dont_need = c('Sample','Multi_BC','Multi_BC_.','Morphotype',barcoder_identifier)
columns_we_need = all_columns[!(all_columns %in% columns_we_dont_need)]
for (feature_name in columns_we_need) {
metadata_old_removed[feature_name]<- my_data_72h[[feature_name]][match(metadata_old_removed$Sample.barcode, my_data_72h[[barcoder_identifier]])]
}
metadata_old_removedactually adding the metadata to the Seurat object. One thing to do beforehand is removing the old morpho data from the seurat object
for (x in old_morpho_features) {
Gastruloid_72h_merged_afterQC@meta.data[[x]]=NULL
}
head(Gastruloid_72h_merged_afterQC@meta.data)Now we can add the new metadata
for (feature_name in columns_we_need){
Gastruloid_72h_merged_afterQC <- AddMetaData(object = Gastruloid_72h_merged_afterQC, metadata = metadata_old_removed[[feature_name]], col.name = feature_name)
}
# Now we can look at the final dataframe:
Gastruloid_72h_merged_afterQC@meta.datachecking the column_names
colnames(Gastruloid_72h_merged_afterQC@meta.data) [1] "orig.ident" "nCount_RNA" "nFeature_RNA"
[4] "Sample.barcode" "Morphotype" "percent.mt"
[7] "RNA_snn_res.0.3" "seurat_clusters" "S.Score"
[10] "G2M.Score" "Phase" "old.ident"
[13] "nCount_SCT" "nFeature_SCT" "predicted.id"
[16] "prediction.score.17" "prediction.score.8" "prediction.score.19"
[19] "prediction.score.3" "prediction.score.37" "prediction.score.13"
[22] "prediction.score.36" "prediction.score.33" "prediction.score.27"
[25] "prediction.score.12" "prediction.score.38" "prediction.score.7"
[28] "prediction.score.2" "prediction.score.11" "prediction.score.20"
[31] "prediction.score.16" "prediction.score.max" "percent.ribo"
[34] "RNA_snn_res.0.5" "RNA_snn_res.0.4" "celltype"
[37] "Emb_Stage" "Plate" "X048h_raw_BF_AreaShape_area"
[40] "X048h_raw_BF_AreaShape_aspect_ratio" "X048h_raw_BF_AreaShape_axis_major_length" "X048h_raw_BF_AreaShape_axis_minor_length"
[43] "X048h_raw_BF_AreaShape_eccentricity" "X048h_raw_BF_AreaShape_feret_diameter_max" "X048h_raw_BF_AreaShape_perimeter"
[46] "X048h_raw_BF_AreaShape_solidity" "X048h_str_BF_AreaShape_area" "X048h_str_BF_AreaShape_aspect_ratio"
[49] "X048h_str_BF_AreaShape_eccentricity" "X048h_str_BF_AreaShape_equivalent_diameter" "X048h_str_BF_AreaShape_extent"
[52] "X048h_str_BF_AreaShape_form_factor" "X048h_str_BF_AreaShape_inertia_tensor_0_0" "X048h_str_BF_AreaShape_inertia_tensor_0_1"
[55] "X048h_str_BF_AreaShape_inertia_tensor_1_0" "X048h_str_BF_AreaShape_inertia_tensor_1_1" "X048h_str_BF_AreaShape_inertia_tensor_eigvals_0"
[58] "X048h_str_BF_AreaShape_inertia_tensor_eigvals_1" "X048h_str_BF_AreaShape_locoefa_PC_1" "X048h_str_BF_AreaShape_locoefa_PC_2"
[61] "X048h_str_BF_AreaShape_locoefa_PC_3" "X048h_str_BF_AreaShape_locoefa_PC_4" "X048h_str_BF_AreaShape_locoefa_PC_5"
[64] "X048h_str_BF_AreaShape_locoefa_UMAP_1" "X048h_str_BF_AreaShape_locoefa_UMAP_2" "X048h_str_BF_AreaShape_locoefa_UMAP_3"
[67] "X048h_str_BF_AreaShape_locoefa_coeff_0" "X048h_str_BF_AreaShape_locoefa_coeff_1" "X048h_str_BF_AreaShape_locoefa_coeff_10"
[70] "X048h_str_BF_AreaShape_locoefa_coeff_11" "X048h_str_BF_AreaShape_locoefa_coeff_12" "X048h_str_BF_AreaShape_locoefa_coeff_13"
[73] "X048h_str_BF_AreaShape_locoefa_coeff_14" "X048h_str_BF_AreaShape_locoefa_coeff_15" "X048h_str_BF_AreaShape_locoefa_coeff_16"
[76] "X048h_str_BF_AreaShape_locoefa_coeff_17" "X048h_str_BF_AreaShape_locoefa_coeff_18" "X048h_str_BF_AreaShape_locoefa_coeff_19"
[79] "X048h_str_BF_AreaShape_locoefa_coeff_2" "X048h_str_BF_AreaShape_locoefa_coeff_20" "X048h_str_BF_AreaShape_locoefa_coeff_21"
[82] "X048h_str_BF_AreaShape_locoefa_coeff_22" "X048h_str_BF_AreaShape_locoefa_coeff_23" "X048h_str_BF_AreaShape_locoefa_coeff_24"
[85] "X048h_str_BF_AreaShape_locoefa_coeff_25" "X048h_str_BF_AreaShape_locoefa_coeff_26" "X048h_str_BF_AreaShape_locoefa_coeff_27"
[88] "X048h_str_BF_AreaShape_locoefa_coeff_28" "X048h_str_BF_AreaShape_locoefa_coeff_29" "X048h_str_BF_AreaShape_locoefa_coeff_3"
[91] "X048h_str_BF_AreaShape_locoefa_coeff_30" "X048h_str_BF_AreaShape_locoefa_coeff_31" "X048h_str_BF_AreaShape_locoefa_coeff_32"
[94] "X048h_str_BF_AreaShape_locoefa_coeff_33" "X048h_str_BF_AreaShape_locoefa_coeff_34" "X048h_str_BF_AreaShape_locoefa_coeff_35"
[97] "X048h_str_BF_AreaShape_locoefa_coeff_36" "X048h_str_BF_AreaShape_locoefa_coeff_37" "X048h_str_BF_AreaShape_locoefa_coeff_38"
[100] "X048h_str_BF_AreaShape_locoefa_coeff_39" "X048h_str_BF_AreaShape_locoefa_coeff_4" "X048h_str_BF_AreaShape_locoefa_coeff_40"
[103] "X048h_str_BF_AreaShape_locoefa_coeff_41" "X048h_str_BF_AreaShape_locoefa_coeff_42" "X048h_str_BF_AreaShape_locoefa_coeff_43"
[106] "X048h_str_BF_AreaShape_locoefa_coeff_44" "X048h_str_BF_AreaShape_locoefa_coeff_45" "X048h_str_BF_AreaShape_locoefa_coeff_46"
[109] "X048h_str_BF_AreaShape_locoefa_coeff_47" "X048h_str_BF_AreaShape_locoefa_coeff_48" "X048h_str_BF_AreaShape_locoefa_coeff_49"
[112] "X048h_str_BF_AreaShape_locoefa_coeff_5" "X048h_str_BF_AreaShape_locoefa_coeff_50" "X048h_str_BF_AreaShape_locoefa_coeff_51"
[115] "X048h_str_BF_AreaShape_locoefa_coeff_6" "X048h_str_BF_AreaShape_locoefa_coeff_7" "X048h_str_BF_AreaShape_locoefa_coeff_8"
[118] "X048h_str_BF_AreaShape_locoefa_coeff_9" "X048h_str_BF_AreaShape_major_axis_length" "X048h_str_BF_AreaShape_minor_axis_length"
[121] "X048h_str_BF_AreaShape_moments_hu_0" "X048h_str_BF_AreaShape_moments_hu_1" "X048h_str_BF_AreaShape_moments_hu_2"
[124] "X048h_str_BF_AreaShape_moments_hu_3" "X048h_str_BF_AreaShape_moments_hu_4" "X048h_str_BF_AreaShape_moments_hu_5"
[127] "X048h_str_BF_AreaShape_moments_hu_6" "X048h_str_BF_AreaShape_orientation" "X048h_str_BF_AreaShape_perimeter"
[130] "X072h_raw_BF_AreaShape_area" "X072h_raw_BF_AreaShape_aspect_ratio" "X072h_raw_BF_AreaShape_axis_major_length"
[133] "X072h_raw_BF_AreaShape_axis_minor_length" "X072h_raw_BF_AreaShape_eccentricity" "X072h_raw_BF_AreaShape_feret_diameter_max"
[136] "X072h_raw_BF_AreaShape_perimeter" "X072h_raw_BF_AreaShape_solidity" "X072h_raw_CH__bf_mask_Intensity_IntegratedIntensity"
[139] "X072h_raw_CH__bf_mask_Intensity_IntegratedIntensityEdge" "X072h_raw_CH__bf_mask_Intensity_LowerQuartileIntensity" "X072h_raw_CH__bf_mask_Intensity_MADIntensity"
[142] "X072h_raw_CH__bf_mask_Intensity_MassDisplacement" "X072h_raw_CH__bf_mask_Intensity_MaxIntensity" "X072h_raw_CH__bf_mask_Intensity_MaxIntensityEdge"
[145] "X072h_raw_CH__bf_mask_Intensity_MeanIntensity" "X072h_raw_CH__bf_mask_Intensity_MeanIntensityEdge" "X072h_raw_CH__bf_mask_Intensity_MedianIntensity"
[148] "X072h_raw_CH__bf_mask_Intensity_MinIntensity" "X072h_raw_CH__bf_mask_Intensity_MinIntensityEdge" "X072h_raw_CH__bf_mask_Intensity_StdIntensity"
[151] "X072h_raw_CH__bf_mask_Intensity_StdIntensityEdge" "X072h_raw_CH__bf_mask_Intensity_UpperQuartileIntensity" "X072h_raw_CH__bf_mask_Location_CenterMassIntensity_X"
[154] "X072h_raw_CH__bf_mask_Location_CenterMassIntensity_Y" "X072h_raw_CH__bf_mask_Location_CenterMassIntensity_Z" "X072h_raw_CH__bf_mask_Location_Center_X"
[157] "X072h_raw_CH__bf_mask_Location_Center_Y" "X072h_raw_CH__bf_mask_Location_Center_Z" "X072h_raw_CH__bf_mask_Location_MaxIntensity_X"
[160] "X072h_raw_CH__bf_mask_Location_MaxIntensity_Y" "X072h_raw_CH__bf_mask_Location_MaxIntensity_Z" "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_1of9"
[163] "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_2of9" "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_3of9" "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_4of9"
[166] "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_5of9" "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_6of9" "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_7of9"
[169] "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_8of9" "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_9of9" "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_1of9"
[172] "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_2of9" "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_3of9" "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_4of9"
[175] "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_5of9" "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_6of9" "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_7of9"
[178] "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_8of9" "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_9of9" "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_1of9"
[181] "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_2of9" "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_3of9" "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_4of9"
[184] "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_5of9" "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_6of9" "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_7of9"
[187] "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_8of9" "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_9of9" "X072h_raw_CH_bra_mask_AreaShape_Area"
[190] "X072h_raw_CH_bra_mask_AreaShape_BoundingBoxArea" "X072h_raw_CH_bra_mask_AreaShape_BoundingBoxMaximum_X" "X072h_raw_CH_bra_mask_AreaShape_BoundingBoxMaximum_Y"
[193] "X072h_raw_CH_bra_mask_AreaShape_BoundingBoxMinimum_X" "X072h_raw_CH_bra_mask_AreaShape_BoundingBoxMinimum_Y" "X072h_raw_CH_bra_mask_AreaShape_Center_X"
[196] "X072h_raw_CH_bra_mask_AreaShape_Center_Y" "X072h_raw_CH_bra_mask_AreaShape_Compactness" "X072h_raw_CH_bra_mask_AreaShape_ConvexArea"
[199] "X072h_raw_CH_bra_mask_AreaShape_Eccentricity" "X072h_raw_CH_bra_mask_AreaShape_EquivalentDiameter" "X072h_raw_CH_bra_mask_AreaShape_EulerNumber"
[202] "X072h_raw_CH_bra_mask_AreaShape_Extent" "X072h_raw_CH_bra_mask_AreaShape_FormFactor" "X072h_raw_CH_bra_mask_AreaShape_MajorAxisLength"
[205] "X072h_raw_CH_bra_mask_AreaShape_MaxFeretDiameter" "X072h_raw_CH_bra_mask_AreaShape_MaximumRadius" "X072h_raw_CH_bra_mask_AreaShape_MeanRadius"
[208] "X072h_raw_CH_bra_mask_AreaShape_MedianRadius" "X072h_raw_CH_bra_mask_AreaShape_MinFeretDiameter" "X072h_raw_CH_bra_mask_AreaShape_MinorAxisLength"
[211] "X072h_raw_CH_bra_mask_AreaShape_Orientation" "X072h_raw_CH_bra_mask_AreaShape_Perimeter" "X072h_raw_CH_bra_mask_AreaShape_Solidity"
[214] "X072h_raw_CH_bra_mask_Intensity_IntegratedIntensity" "X072h_raw_CH_bra_mask_Intensity_IntegratedIntensityEdge" "X072h_raw_CH_bra_mask_Intensity_LowerQuartileIntensity"
[217] "X072h_raw_CH_bra_mask_Intensity_MADIntensity" "X072h_raw_CH_bra_mask_Intensity_MassDisplacement" "X072h_raw_CH_bra_mask_Intensity_MaxIntensity"
[220] "X072h_raw_CH_bra_mask_Intensity_MaxIntensityEdge" "X072h_raw_CH_bra_mask_Intensity_MeanIntensity" "X072h_raw_CH_bra_mask_Intensity_MeanIntensityEdge"
[223] "X072h_raw_CH_bra_mask_Intensity_MedianIntensity" "X072h_raw_CH_bra_mask_Intensity_MinIntensity" "X072h_raw_CH_bra_mask_Intensity_MinIntensityEdge"
[226] "X072h_raw_CH_bra_mask_Intensity_StdIntensity" "X072h_raw_CH_bra_mask_Intensity_StdIntensityEdge" "X072h_raw_CH_bra_mask_Intensity_UpperQuartileIntensity"
[229] "X072h_raw_CH_bra_mask_Location_CenterMassIntensity_X" "X072h_raw_CH_bra_mask_Location_CenterMassIntensity_Y" "X072h_raw_CH_bra_mask_Location_CenterMassIntensity_Z"
[232] "X072h_raw_CH_bra_mask_Location_Center_X" "X072h_raw_CH_bra_mask_Location_Center_Y" "X072h_raw_CH_bra_mask_Location_Center_Z"
[235] "X072h_raw_CH_bra_mask_Location_MaxIntensity_X" "X072h_raw_CH_bra_mask_Location_MaxIntensity_Y" "X072h_raw_CH_bra_mask_Location_MaxIntensity_Z"
[238] "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_1of9" "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_2of9" "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_3of9"
[241] "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_4of9" "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_5of9" "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_6of9"
[244] "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_7of9" "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_8of9" "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_9of9"
[247] "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_1of9" "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_2of9" "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_3of9"
[250] "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_4of9" "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_5of9" "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_6of9"
[253] "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_7of9" "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_8of9" "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_9of9"
[256] "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_1of9" "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_2of9" "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_3of9"
[259] "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_4of9" "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_5of9" "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_6of9"
[262] "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_7of9" "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_8of9" "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_9of9"
[265] "X072h_str_BF_AreaShape_area" "X072h_str_BF_AreaShape_aspect_ratio" "X072h_str_BF_AreaShape_eccentricity"
[268] "X072h_str_BF_AreaShape_equivalent_diameter" "X072h_str_BF_AreaShape_extent" "X072h_str_BF_AreaShape_form_factor"
[271] "X072h_str_BF_AreaShape_inertia_tensor_0_0" "X072h_str_BF_AreaShape_inertia_tensor_0_1" "X072h_str_BF_AreaShape_inertia_tensor_1_0"
[274] "X072h_str_BF_AreaShape_inertia_tensor_1_1" "X072h_str_BF_AreaShape_inertia_tensor_eigvals_0" "X072h_str_BF_AreaShape_inertia_tensor_eigvals_1"
[277] "X072h_str_BF_AreaShape_locoefa_PC_1" "X072h_str_BF_AreaShape_locoefa_PC_2" "X072h_str_BF_AreaShape_locoefa_PC_3"
[280] "X072h_str_BF_AreaShape_locoefa_PC_4" "X072h_str_BF_AreaShape_locoefa_PC_5" "X072h_str_BF_AreaShape_locoefa_UMAP_1"
[283] "X072h_str_BF_AreaShape_locoefa_UMAP_2" "X072h_str_BF_AreaShape_locoefa_UMAP_3" "X072h_str_BF_AreaShape_locoefa_coeff_0"
[286] "X072h_str_BF_AreaShape_locoefa_coeff_1" "X072h_str_BF_AreaShape_locoefa_coeff_10" "X072h_str_BF_AreaShape_locoefa_coeff_11"
[289] "X072h_str_BF_AreaShape_locoefa_coeff_12" "X072h_str_BF_AreaShape_locoefa_coeff_13" "X072h_str_BF_AreaShape_locoefa_coeff_14"
[292] "X072h_str_BF_AreaShape_locoefa_coeff_15" "X072h_str_BF_AreaShape_locoefa_coeff_16" "X072h_str_BF_AreaShape_locoefa_coeff_17"
[295] "X072h_str_BF_AreaShape_locoefa_coeff_18" "X072h_str_BF_AreaShape_locoefa_coeff_19" "X072h_str_BF_AreaShape_locoefa_coeff_2"
[298] "X072h_str_BF_AreaShape_locoefa_coeff_20" "X072h_str_BF_AreaShape_locoefa_coeff_21" "X072h_str_BF_AreaShape_locoefa_coeff_22"
[301] "X072h_str_BF_AreaShape_locoefa_coeff_23" "X072h_str_BF_AreaShape_locoefa_coeff_24" "X072h_str_BF_AreaShape_locoefa_coeff_25"
[304] "X072h_str_BF_AreaShape_locoefa_coeff_26" "X072h_str_BF_AreaShape_locoefa_coeff_27" "X072h_str_BF_AreaShape_locoefa_coeff_28"
[307] "X072h_str_BF_AreaShape_locoefa_coeff_29" "X072h_str_BF_AreaShape_locoefa_coeff_3" "X072h_str_BF_AreaShape_locoefa_coeff_30"
[310] "X072h_str_BF_AreaShape_locoefa_coeff_31" "X072h_str_BF_AreaShape_locoefa_coeff_32" "X072h_str_BF_AreaShape_locoefa_coeff_33"
[313] "X072h_str_BF_AreaShape_locoefa_coeff_34" "X072h_str_BF_AreaShape_locoefa_coeff_35" "X072h_str_BF_AreaShape_locoefa_coeff_36"
[316] "X072h_str_BF_AreaShape_locoefa_coeff_37" "X072h_str_BF_AreaShape_locoefa_coeff_38" "X072h_str_BF_AreaShape_locoefa_coeff_39"
[319] "X072h_str_BF_AreaShape_locoefa_coeff_4" "X072h_str_BF_AreaShape_locoefa_coeff_40" "X072h_str_BF_AreaShape_locoefa_coeff_41"
[322] "X072h_str_BF_AreaShape_locoefa_coeff_42" "X072h_str_BF_AreaShape_locoefa_coeff_43" "X072h_str_BF_AreaShape_locoefa_coeff_44"
[325] "X072h_str_BF_AreaShape_locoefa_coeff_45" "X072h_str_BF_AreaShape_locoefa_coeff_46" "X072h_str_BF_AreaShape_locoefa_coeff_47"
[328] "X072h_str_BF_AreaShape_locoefa_coeff_48" "X072h_str_BF_AreaShape_locoefa_coeff_49" "X072h_str_BF_AreaShape_locoefa_coeff_5"
[331] "X072h_str_BF_AreaShape_locoefa_coeff_50" "X072h_str_BF_AreaShape_locoefa_coeff_51" "X072h_str_BF_AreaShape_locoefa_coeff_6"
[334] "X072h_str_BF_AreaShape_locoefa_coeff_7" "X072h_str_BF_AreaShape_locoefa_coeff_8" "X072h_str_BF_AreaShape_locoefa_coeff_9"
[337] "X072h_str_BF_AreaShape_major_axis_length" "X072h_str_BF_AreaShape_minor_axis_length" "X072h_str_BF_AreaShape_moments_hu_0"
[340] "X072h_str_BF_AreaShape_moments_hu_1" "X072h_str_BF_AreaShape_moments_hu_2" "X072h_str_BF_AreaShape_moments_hu_3"
[343] "X072h_str_BF_AreaShape_moments_hu_4" "X072h_str_BF_AreaShape_moments_hu_5" "X072h_str_BF_AreaShape_moments_hu_6"
[346] "X072h_str_BF_AreaShape_orientation" "X072h_str_BF_AreaShape_perimeter" "X072h_str_CH_AreaShape_Bra_MajorAxis_Polarisation"
[349] "X072h_str_CH_AreaShape_Bra_MinorAxis_Polarisation" "X096h_raw_BF_AreaShape_area" "X096h_raw_BF_AreaShape_aspect_ratio"
[352] "X096h_raw_BF_AreaShape_axis_major_length" "X096h_raw_BF_AreaShape_axis_minor_length" "X096h_raw_BF_AreaShape_eccentricity"
[355] "X096h_raw_BF_AreaShape_feret_diameter_max" "X096h_raw_BF_AreaShape_perimeter" "X096h_raw_BF_AreaShape_solidity"
[358] "X096h_raw_CH_AreaShape_Bra_AreaFraction" "X096h_raw_CH__bf_mask_Intensity_IntegratedIntensity" "X096h_raw_CH__bf_mask_Intensity_IntegratedIntensityEdge"
[361] "X096h_raw_CH__bf_mask_Intensity_LowerQuartileIntensity" "X096h_raw_CH__bf_mask_Intensity_MADIntensity" "X096h_raw_CH__bf_mask_Intensity_MassDisplacement"
[364] "X096h_raw_CH__bf_mask_Intensity_MaxIntensity" "X096h_raw_CH__bf_mask_Intensity_MaxIntensityEdge" "X096h_raw_CH__bf_mask_Intensity_MeanIntensity"
[367] "X096h_raw_CH__bf_mask_Intensity_MeanIntensityEdge" "X096h_raw_CH__bf_mask_Intensity_MedianIntensity" "X096h_raw_CH__bf_mask_Intensity_MinIntensity"
[370] "X096h_raw_CH__bf_mask_Intensity_MinIntensityEdge" "X096h_raw_CH__bf_mask_Intensity_StdIntensity" "X096h_raw_CH__bf_mask_Intensity_StdIntensityEdge"
[373] "X096h_raw_CH__bf_mask_Intensity_UpperQuartileIntensity" "X096h_raw_CH__bf_mask_Location_CenterMassIntensity_X" "X096h_raw_CH__bf_mask_Location_CenterMassIntensity_Y"
[376] "X096h_raw_CH__bf_mask_Location_CenterMassIntensity_Z" "X096h_raw_CH__bf_mask_Location_Center_X" "X096h_raw_CH__bf_mask_Location_Center_Y"
[379] "X096h_raw_CH__bf_mask_Location_Center_Z" "X096h_raw_CH__bf_mask_Location_MaxIntensity_X" "X096h_raw_CH__bf_mask_Location_MaxIntensity_Y"
[382] "X096h_raw_CH__bf_mask_Location_MaxIntensity_Z" "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_1of9" "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_2of9"
[385] "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_3of9" "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_4of9" "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_5of9"
[388] "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_6of9" "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_7of9" "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_8of9"
[391] "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_9of9" "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_1of9" "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_2of9"
[394] "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_3of9" "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_4of9" "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_5of9"
[397] "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_6of9" "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_7of9" "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_8of9"
[400] "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_9of9" "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_1of9" "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_2of9"
[403] "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_3of9" "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_4of9" "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_5of9"
[406] "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_6of9" "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_7of9" "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_8of9"
[409] "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_9of9" "X096h_raw_CH_bra_mask_AreaShape_Area" "X096h_raw_CH_bra_mask_AreaShape_BoundingBoxArea"
[412] "X096h_raw_CH_bra_mask_AreaShape_BoundingBoxMaximum_X" "X096h_raw_CH_bra_mask_AreaShape_BoundingBoxMaximum_Y" "X096h_raw_CH_bra_mask_AreaShape_BoundingBoxMinimum_X"
[415] "X096h_raw_CH_bra_mask_AreaShape_BoundingBoxMinimum_Y" "X096h_raw_CH_bra_mask_AreaShape_Center_X" "X096h_raw_CH_bra_mask_AreaShape_Center_Y"
[418] "X096h_raw_CH_bra_mask_AreaShape_Compactness" "X096h_raw_CH_bra_mask_AreaShape_ConvexArea" "X096h_raw_CH_bra_mask_AreaShape_Eccentricity"
[421] "X096h_raw_CH_bra_mask_AreaShape_EquivalentDiameter" "X096h_raw_CH_bra_mask_AreaShape_EulerNumber" "X096h_raw_CH_bra_mask_AreaShape_Extent"
[424] "X096h_raw_CH_bra_mask_AreaShape_FormFactor" "X096h_raw_CH_bra_mask_AreaShape_MajorAxisLength" "X096h_raw_CH_bra_mask_AreaShape_MaxFeretDiameter"
[427] "X096h_raw_CH_bra_mask_AreaShape_MaximumRadius" "X096h_raw_CH_bra_mask_AreaShape_MeanRadius" "X096h_raw_CH_bra_mask_AreaShape_MedianRadius"
[430] "X096h_raw_CH_bra_mask_AreaShape_MinFeretDiameter" "X096h_raw_CH_bra_mask_AreaShape_MinorAxisLength" "X096h_raw_CH_bra_mask_AreaShape_Orientation"
[433] "X096h_raw_CH_bra_mask_AreaShape_Perimeter" "X096h_raw_CH_bra_mask_AreaShape_Solidity" "X096h_raw_CH_bra_mask_Intensity_IntegratedIntensity"
[436] "X096h_raw_CH_bra_mask_Intensity_IntegratedIntensityEdge" "X096h_raw_CH_bra_mask_Intensity_LowerQuartileIntensity" "X096h_raw_CH_bra_mask_Intensity_MADIntensity"
[439] "X096h_raw_CH_bra_mask_Intensity_MassDisplacement" "X096h_raw_CH_bra_mask_Intensity_MaxIntensity" "X096h_raw_CH_bra_mask_Intensity_MaxIntensityEdge"
[442] "X096h_raw_CH_bra_mask_Intensity_MeanIntensity" "X096h_raw_CH_bra_mask_Intensity_MeanIntensityEdge" "X096h_raw_CH_bra_mask_Intensity_MedianIntensity"
[445] "X096h_raw_CH_bra_mask_Intensity_MinIntensity" "X096h_raw_CH_bra_mask_Intensity_MinIntensityEdge" "X096h_raw_CH_bra_mask_Intensity_StdIntensity"
[448] "X096h_raw_CH_bra_mask_Intensity_StdIntensityEdge" "X096h_raw_CH_bra_mask_Intensity_UpperQuartileIntensity" "X096h_raw_CH_bra_mask_Location_CenterMassIntensity_X"
[451] "X096h_raw_CH_bra_mask_Location_CenterMassIntensity_Y" "X096h_raw_CH_bra_mask_Location_CenterMassIntensity_Z" "X096h_raw_CH_bra_mask_Location_Center_X"
[454] "X096h_raw_CH_bra_mask_Location_Center_Y" "X096h_raw_CH_bra_mask_Location_Center_Z" "X096h_raw_CH_bra_mask_Location_MaxIntensity_X"
[457] "X096h_raw_CH_bra_mask_Location_MaxIntensity_Y" "X096h_raw_CH_bra_mask_Location_MaxIntensity_Z" "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_1of9"
[460] "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_2of9" "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_3of9" "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_4of9"
[463] "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_5of9" "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_6of9" "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_7of9"
[466] "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_8of9" "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_9of9" "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_1of9"
[469] "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_2of9" "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_3of9" "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_4of9"
[472] "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_5of9" "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_6of9" "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_7of9"
[475] "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_8of9" "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_9of9" "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_1of9"
[478] "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_2of9" "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_3of9" "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_4of9"
[481] "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_5of9" "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_6of9" "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_7of9"
[484] "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_8of9" "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_9of9" "X096h_str_BF_AreaShape_area"
[487] "X096h_str_BF_AreaShape_aspect_ratio" "X096h_str_BF_AreaShape_eccentricity" "X096h_str_BF_AreaShape_equivalent_diameter"
[490] "X096h_str_BF_AreaShape_extent" "X096h_str_BF_AreaShape_form_factor" "X096h_str_BF_AreaShape_inertia_tensor_0_0"
[493] "X096h_str_BF_AreaShape_inertia_tensor_0_1" "X096h_str_BF_AreaShape_inertia_tensor_1_0" "X096h_str_BF_AreaShape_inertia_tensor_1_1"
[496] "X096h_str_BF_AreaShape_inertia_tensor_eigvals_0" "X096h_str_BF_AreaShape_inertia_tensor_eigvals_1" "X096h_str_BF_AreaShape_locoefa_PC_1"
[499] "X096h_str_BF_AreaShape_locoefa_PC_2" "X096h_str_BF_AreaShape_locoefa_PC_3" "X096h_str_BF_AreaShape_locoefa_PC_4"
[502] "X096h_str_BF_AreaShape_locoefa_PC_5" "X096h_str_BF_AreaShape_locoefa_UMAP_1" "X096h_str_BF_AreaShape_locoefa_UMAP_2"
[505] "X096h_str_BF_AreaShape_locoefa_UMAP_3" "X096h_str_BF_AreaShape_locoefa_coeff_0" "X096h_str_BF_AreaShape_locoefa_coeff_1"
[508] "X096h_str_BF_AreaShape_locoefa_coeff_10" "X096h_str_BF_AreaShape_locoefa_coeff_11" "X096h_str_BF_AreaShape_locoefa_coeff_12"
[511] "X096h_str_BF_AreaShape_locoefa_coeff_13" "X096h_str_BF_AreaShape_locoefa_coeff_14" "X096h_str_BF_AreaShape_locoefa_coeff_15"
[514] "X096h_str_BF_AreaShape_locoefa_coeff_16" "X096h_str_BF_AreaShape_locoefa_coeff_17" "X096h_str_BF_AreaShape_locoefa_coeff_18"
[517] "X096h_str_BF_AreaShape_locoefa_coeff_19" "X096h_str_BF_AreaShape_locoefa_coeff_2" "X096h_str_BF_AreaShape_locoefa_coeff_20"
[520] "X096h_str_BF_AreaShape_locoefa_coeff_21" "X096h_str_BF_AreaShape_locoefa_coeff_22" "X096h_str_BF_AreaShape_locoefa_coeff_23"
[523] "X096h_str_BF_AreaShape_locoefa_coeff_24" "X096h_str_BF_AreaShape_locoefa_coeff_25" "X096h_str_BF_AreaShape_locoefa_coeff_26"
[526] "X096h_str_BF_AreaShape_locoefa_coeff_27" "X096h_str_BF_AreaShape_locoefa_coeff_28" "X096h_str_BF_AreaShape_locoefa_coeff_29"
[529] "X096h_str_BF_AreaShape_locoefa_coeff_3" "X096h_str_BF_AreaShape_locoefa_coeff_30" "X096h_str_BF_AreaShape_locoefa_coeff_31"
[532] "X096h_str_BF_AreaShape_locoefa_coeff_32" "X096h_str_BF_AreaShape_locoefa_coeff_33" "X096h_str_BF_AreaShape_locoefa_coeff_34"
[535] "X096h_str_BF_AreaShape_locoefa_coeff_35" "X096h_str_BF_AreaShape_locoefa_coeff_36" "X096h_str_BF_AreaShape_locoefa_coeff_37"
[538] "X096h_str_BF_AreaShape_locoefa_coeff_38" "X096h_str_BF_AreaShape_locoefa_coeff_39" "X096h_str_BF_AreaShape_locoefa_coeff_4"
[541] "X096h_str_BF_AreaShape_locoefa_coeff_40" "X096h_str_BF_AreaShape_locoefa_coeff_41" "X096h_str_BF_AreaShape_locoefa_coeff_42"
[544] "X096h_str_BF_AreaShape_locoefa_coeff_43" "X096h_str_BF_AreaShape_locoefa_coeff_44" "X096h_str_BF_AreaShape_locoefa_coeff_45"
[547] "X096h_str_BF_AreaShape_locoefa_coeff_46" "X096h_str_BF_AreaShape_locoefa_coeff_47" "X096h_str_BF_AreaShape_locoefa_coeff_48"
[550] "X096h_str_BF_AreaShape_locoefa_coeff_49" "X096h_str_BF_AreaShape_locoefa_coeff_5" "X096h_str_BF_AreaShape_locoefa_coeff_50"
[553] "X096h_str_BF_AreaShape_locoefa_coeff_51" "X096h_str_BF_AreaShape_locoefa_coeff_6" "X096h_str_BF_AreaShape_locoefa_coeff_7"
[556] "X096h_str_BF_AreaShape_locoefa_coeff_8" "X096h_str_BF_AreaShape_locoefa_coeff_9" "X096h_str_BF_AreaShape_major_axis_length"
[559] "X096h_str_BF_AreaShape_minor_axis_length" "X096h_str_BF_AreaShape_moments_hu_0" "X096h_str_BF_AreaShape_moments_hu_1"
[562] "X096h_str_BF_AreaShape_moments_hu_2" "X096h_str_BF_AreaShape_moments_hu_3" "X096h_str_BF_AreaShape_moments_hu_4"
[565] "X096h_str_BF_AreaShape_moments_hu_5" "X096h_str_BF_AreaShape_moments_hu_6" "X096h_str_BF_AreaShape_orientation"
[568] "X096h_str_BF_AreaShape_perimeter" "X096h_str_CH_AreaShape_Bra_MajorAxis_Polarisation" "X096h_str_CH_AreaShape_Bra_MinorAxis_Polarisation" Now we can save this monstrosity to disc:
saveRDS(Gastruloid_72h_merged_afterQC, file = "df72v3_updated_morphodata.rds")